tapir

About

TAPIR (Tally Approximations of Phylogenetic Informativeness
Rapidly) is a set of programs used to estimate and plot
phylogenetic informativeness for large datasets.

Versions and Availability

▶ Display Softenv Keys for tapir on all clusters

Machine

Version

Softenv Key

supermike2

1.0

+tapir-1.0-gcc-4.4.6-python-2.7.3

▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex
user environments with potentially conflicting application versions
and libraries.

System Default Path

When a user logs in, the system /etc/profile
or /etc/csh.cshrc (depending on login shell, and mirrored
from csm:/cfmroot/etc/profile)
calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to
set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the
variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of
available packages. The listing will look something like:

Managing SoftEnv

The file ~/.soft in the user's home directory is where
the different packages are managed. Add the +keyword into your .soft
file. For instance, ff one wants to add the Amber Molecular Dynamics
package into their environment, the end of the .soft file should look
like this:

+amber-8

@default

To update the environment after modifying this file, one simply
uses the resoft command:

% resoft

The command soft can be used to manipulate the environment
from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user
to pay attention to possible order dependencies. That is, best results
require the user to remove keywords in the reverse order in which they
were added. It is handy to test out individual keys, but can lead to
trouble if changing multiple keys. Changing the .soft file and
issuing the resoft is the recommended way of dealing with
multiple changes.

▶ Display Module Names for tapir on all clusters.

Machine

Version

Module

None Available

N/A

N/A

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash
and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if
they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR
will cause things like rsync to break)

~/.bashrc (interactive login only)

~/.profile

When a user logs out of an interactive session, the
file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is
set automatically using SoftEnv. See below for more
information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's
environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business
of setting up their shell environment in the face of potentially
conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules
in their home directory. This file contains module commands to
set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look
something like: